INFSO-RI Enabling Grids for E-sciencE An MRI Simulation Web Portal on EGEE Grid Architecture F. Bellet, I. Nistoreanu, C. Pera, H. Benoit-Cattin CREATIS, UMR CNRS #5515, U630 Inserm, FRANCE

Enabling Grids for E-sciencE INFSO-RI EGEE User Forum, March /10 Why MRI Simulation ? – Better understanding of the complexity of MRI imaging – Pedagogic purposes – Conception, calibration and test of MRI sequences in-silico. – Generation of MRI images with a “ground truth”  Artefacts impact and correction  MR Image processing validation (segmentation, quantification) Previous works – 1D MRI simulation [Bittoun-81] – 2D MRI simulation [Olsson-95] – Simulation with a distributed implementation [Brenner-97] – 3D brain MRI simulation [Kwan-99] – Susceptibility and MRI simulation [Yoder-02-04]

Enabling Grids for E-sciencE INFSO-RI EGEE User Forum, March /10 Virtual object (i,ρ,T 1,T 2 ) MRI Image FFT based reconstruction Magnetization process kernel K-space RF signals MRI sequence - RF Pulse - Gradient - Precession - Acquisition Bo + ∆B map Filtering Acquisition noise model Kernel implements Bloch’s electromagnetism equation Huge computation time (512 2 = 12h, > 100 years !) Parallel implementation > MPI SIMRI Overview

Enabling Grids for E-sciencE INFSO-RI EGEE User Forum, March /10 June 2001 : SIMRI Project start June 2002 : Parallelisation of the magnetization kernel Dec : Cluster deployment June 2003: SpinPlayer : 1D interactive simulation interface Nov : Grid deployment 2004 : Artefacts simulation (Susceptibility, Chemical shift, field default) Dec 2004 : New parallelisation scheme at a sequence level March 2005 : Major publication in J. Magnetic Resonance June 2005 : : Simulation web portal Nov: 2005 : SIMRI distribution under CECILL public licence DATAGRID EGEE SIMRI Milestones

Enabling Grids for E-sciencE INFSO-RI EGEE User Forum, March /10 Grid added value – Speeds up the simulation time by a factor linked to the node number – Enables simulation of high resolution images – Enables simultaneous simulation to a wide user community Grid key issues – Homogenisation of MPI implementation on the grid clusters. – Enabling job submission to multiple clusters to get numerous nodes for 3D simulation. – Enhancement of scheduling to estimate job termination. – Providing of web portals to mask the middleware to final users – Facilitation of the server certificate usage. SIMRI : A grid experience

Enabling Grids for E-sciencE INFSO-RI EGEE User Forum, March /10 Functionalities – Full simulation access (all simulation parameters) – Two simulation targets : EGEE grid (LCG2), Local Cluster (PBS) – User authentification – Enhanced user job history, Enhanced running job status – Simulation results sent by mail Status and evolution – At the moment, only open to the 10 SIMRI developers – Autumn 2006: Version 2  Web service architecture, associated to Glite  Enhanced interface  New simulation target : CINES, SGI multiproc – Progressive simulation service opening to all the scientific community Web portal

Enabling Grids for E-sciencE INFSO-RI EGEE User Forum, March /10 Web portal Technical context – Serveur Web Apache v – Module PHP5 (libssh2.so et mysql.so) – MySql v.4 – Java (jsch.jar,mysql-connector-java-3.jar) – MPI and batch managers (LCG2, PBS) Architecture – Three layers architecture  Presentation layer (PHP)  Process Layer User management (Apache) Job management (JavaThread)  Data Layer (MySql) : user and job data Client Job submission Web server Simri JobServer Job add Targeted platform JAVA Thread

Enabling Grids for E-sciencE INFSO-RI EGEE User Forum, March /10 illustration

Enabling Grids for E-sciencE INFSO-RI EGEE User Forum, March /10 SIMRI Facts Software – The most advanced available MRI simulator : 1D, 2D, 3D, field default, Chemical shift, T 2 * management … – Distributed under the public CECILL License (> 100 download within 30 labs) – Simulation service proposed through a web portal connected to EGEE grid Publications – H. Benoit-Cattin et al. "The SIMRI project: A versatile and interactive MRI simulator," Journal of Magnetic Resonance, vol. 173, pp , – J. Montagnat et al. "Medical images simulation, storage, and processing on the European DataGrid testbed," Journal of Grid Computing, vol. 2, pp , – H. Benoit-Cattin et al. "Magnetic Resonance Imaging (MRI) simulation on a grid computing architecture,"IEEE CGIGRID'03- BIOGRID'03, Tokyo,  B. Belaroussi et al. "Distortion correction for susceptibility-induced artifacts in spin echo MR images: Simulation study at 1.5 T and 7 T.,"Proc. ISMRM'04.  B. Belaroussi et al. "Susceptibility artifact correction in GE images,"Proc. ISMRM'06.

Enabling Grids for E-sciencE INFSO-RI EGEE User Forum, March /10 SIMRI perpectives Simulation features – Take benefit of the code diffusion to enlarge the user community and to get contributions in :  New anatomical objects  New MRI sequences  New simulation model (diffusion, antennas, pulse …) Simulation services – Open widely the SIMRI grid portal. – Turn the portal architecture to an evolutive web service one. – Provide a data management service associated to the high value simulated images – Think about a multimodality (MRI, CT, PET, US) Medical Image simulation portal.